Visualizing viral infection and the ensuing immune response provides unique insights into viral pathogenesis as well as immune-mediated viral clearance. Using a variety of imaging modalities, including ex vivo analysis of frozen tissue sections as well as in vivo multiphoton microscopy, we have been imaging viral infection of the lymph node, skin, spleen, liver, and ovaries. We create fluorescent-protein expressing viruses and fluorescently tagged virions to explore viral infection and spread in the tissue, and we use fluorescent reporter mice identifying different immune cell populations to visualize the behavior of cells in virus-infected tissue. These studies provide fundamental knowledge of the pathogenesis and clearance of vaccinia virus, influenza virus, zika virus, and sindbis virus which can then be applied to rational vaccine or therapeutic design.